Alu elements are primate-specific SINE mobile elements (Short, INterspersed Elements). They have amplified over the past 65 million years to the point where they occupy about 11% of the human genome, with well over 1 million copies per genome. They have been a major force in shaping the primate genome and whose insertion continues to cause approximately one in a thousand new human genetic diseases. In addition, once inserted, they continue to lead to mutations that affect gene splicing, triplet repeat diseases, and unequal Alu/Alu recombination, whiclvleads to a much higher level of disease. Studies on L1 elements are increasingly implicating human mobile elements in genetic damage to somatic cells. Thus, mobile elements are likely to represent one of the most important intrinsic factors contributing to genetic instability in both germ-line genetic disease, as well as somatic mutations leading to aging and diseases, such as cancer. Almost all current activity from Alu elements comes from a very small proportion of active elements. It is critical that we determine which features determine whether an Alu is active. This will allow us to determine whether some individuals are more prone to mobile element damage than others, or even suggest approaches to controlling that damage. We have also found that Alu elements can potentially be active under conditions where other human elements are not, making it important to characterize all of the major human mobile elements. Our specific aims are: 1. To determine which aspects of the RNA produced by different Alu loci influence their relative activity in order to understand the approximately 4000-fold selection for activity by young Alu elements. We will specifically assess the role of A-tail length and heterogeneity, Alu subfamily mutations, as well as random mutations that might affect the RNA structure, and the 3'unique regions that will differ between different Alu loci. 2. To utilize new approaches to determine the diversity and levels of Alu RNA expression from different normal tissues. These studies will help us assess how many loci express in a given tissue and whether the loci differ between tissues. 3. We will utilize an approach that allows an assessment of specific aspects of Alu elements (such as transcription strength, A-tail length, mismatch, spacing etc.) to contribute to Alu/Alu unequal homologous recombination. These studies will help to shed light on the reasons why some genetic loci are particularly prone to this form of recombination and whether we can better predict regions of genetic instability in the genome.